Fig. 4: Agent-based models reproduce complex pathway dynamics whilst incorporating spatial information. | npj Systems Biology and Applications

Fig. 4: Agent-based models reproduce complex pathway dynamics whilst incorporating spatial information.

From: The FLAME-accelerated signalling tool (FaST) for facile parallelisation of flexible agent-based models of cell signalling

Fig. 4

ABM simulations (solid lines) of apoptosis execution were compared to equivalent ODE simulations (dashed lines) for pro, activated or complex forms of caspase 9 (a); pro, activated or complex forms of caspase 3 (b); and XIAP or SMAC complexes (c). Visualisations of a single simulation were captured at 0, 7.5, 15 and 30 mins. All simulations were for 30 min, the time step Δt for particle diffusion was 0.0001 s and for reactions was 0.05 s in all simulations. Data in a–c represent results from a single simulation. Data in b represents mean +/− range (thin grey lines) from three independent simulations.

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